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Are you saying that 03.nef is

Are you saying that 03.nef is underexposed and the dcraw rendering is normal?
Then the question remains, how did rawtherapee know how to compensate?

Here is a Sony A7 raw, the corresponding 'out of the camera' jpeg, and renderings by dcraw and rawtherapee:

The rawtherapee rendering and the 'out of the camera' jpeg are nearly identical, whereas the dcraw rendering is too dark. Is this normal and expected? (my libraw implementation gives the same result as dcraw).

dcraw -w -T DSC00574.ARW
rawtherapee-cli -t -b8 -d -c DSC00574.ARW

Source web page for the above raw and jpeg: